5YD8: Human PCNA

Crystal structure of human PCNA in complex with APIM of human ZRANB3. Determined by X-ray diffraction at 2.3 Å resolution. Released 18 Apr 2018.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 6
Atoms: 5,933
Mol. weight: 90.19 kDa
Released: 18 Apr 2018

Explore 5YD8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YD8 contains 30 α-helices and 61 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain U: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	1070	1	7
α-helix	1073-1075	3
β-strand	1077-1078	2	5

Chains V and W: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1073-1075	3

Chain X: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	3
α-helix	10-17	8
β-strand	25-31	7	4
β-strand	34-40	7	4
β-strand	46-53	8	4
α-helix	54-56	3
β-strand	59-62	4	3
β-strand	66-71	6	4
α-helix	72-79	8
β-strand	87-92	6	3
β-strand	98-104	7	3
β-strand	110-117	8	3
β-strand	119	1	4
β-strand	126-127	2	5
α-helix	128-130	3
β-strand	135-140	6	4
α-helix	141-152	12
β-strand	157-162	6	6
β-strand	166-172	7	6
β-strand	176-183	8	6
β-strand	196-199	4	4
β-strand	203-208	6	6
α-helix	209-215	7
α-helix	216-221	6
β-strand	224-229	6	4
β-strand	235-241	7	4
β-strand	245-251	7	4
α-helix	252-253	2
β-strand	254	1	7

Chain Y: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	10-19	10
β-strand	25-31	7	2
β-strand	34-40	7	2
β-strand	46-53	8	2
α-helix	54-56	3
β-strand	59-62	4	1
β-strand	66-71	6	2
α-helix	72-79	8
β-strand	88-92	5	1
β-strand	98-103	6	1
β-strand	110-117	8	1
α-helix	118	1
β-strand	119	1	2
α-helix	128-130	3
β-strand	135-140	6	2
α-helix	141-151	11
β-strand	157-163	7	3
β-strand	166-172	7	3
β-strand	176-183	8	3
α-helix	184-185	2
α-helix	191-193	3
β-strand	196-199	4	2
β-strand	203-208	6	3
α-helix	209-215	7
α-helix	216-221	6
β-strand	224-229	6	2
β-strand	235-241	7	2
β-strand	245-251	7	2

Chain Z: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	6
α-helix	10-20	11
β-strand	25-31	7	8
β-strand	34-40	7	8
β-strand	46-53	8	8
α-helix	54-56	3
β-strand	57-62	6	6
β-strand	66-71	6	8
α-helix	72-79	8
β-strand	87-92	6	6
β-strand	98-104	7	6
β-strand	110-117	8	6
α-helix	118	1
β-strand	119	1	8
α-helix	128-130	3
β-strand	135-140	6	8
α-helix	141-151	11
β-strand	157-162	6	1
β-strand	166-173	8	1
β-strand	176-183	8	1
β-strand	196-199	4	8
β-strand	203-208	6	1
α-helix	209-215	7
α-helix	216-221	6
β-strand	224-229	6	8
β-strand	235-240	6	8
β-strand	245-251	7	8
α-helix	252-254	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proliferating cell nuclear antigen	X, Y, Z	protein	261	Homo sapiens	P12004 (AlphaFold model)
ZRANB3	U, V, W	protein	11	Homo sapiens	Q5FWF4 (AlphaFold model)

Sequence of entity 1 (X, Y, Z), FASTA

>5YD8_1 Proliferating cell nuclear antigen (chains X, Y, Z)
MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTY
RCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMD
LDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNI
KLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYK
IADMGHLKYYLAPKIEDEEGS

Sequence of entity 2 (U, V, W), FASTA

>5YD8_2 ZRANB3 (chains U, V, W)
GSDITRFLVKK

Primary citation

Structure of proliferating cell nuclear antigen (PCNA) bound to an APIM peptide reveals the universality of PCNA interaction. Hara, K., Uchida, M., Tagata, R. et al. Acta Crystallogr F Struct Biol Commun (2018) 74:214-221. DOI 10.1107/S2053230X18003242 · PubMed

Other PDB entries of the same protein (UniProt P12004 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1U7B 1.88 Å, Crystal structure of hPCNA bound to residues 331-350 of the flap endonuclease-1 (FEN1)
8F5Q 1.9 Å, Crystal structure of human PCNA in complex with the PIP box of FBH1
9N3L 1.9 Å, Co-crystal structure of PCNA bound to HSP90alpha inhibitor, SNX2112
5E0U 1.93 Å, Human PCNA variant (S228I) complexed with p21 at 1.9 Angstroms
5MLO 1.96 Å, Crystal structure of human PCNA in complex with ZRANB3 PIP box peptide
4RJF 2.01 Å, Crystal structure of the human sliding clamp at 2.0 angstrom resolution
5E0V 2.07 Å, Human PCNA variant (S228I) complexed with FEN1 at 2.1 Angstroms
3VKX 2.1 Å, Structure of PCNA
6HVO 2.1 Å, Crystal structure of human PCNA in complex with three peptides of p12 subunit of human…
4ZTD 2.2 Å, Crystal Structure of Human PCNA in complex with a TRAIP peptide
5YCO 2.2 Å, Complex structure of PCNA with UHRF2
5MOM 2.27 Å, Crystal Structure of PCNA encoding the hypomorphic mutation S228I

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